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The gut microbiota has emerged as a factor that influences exercise performance and recovery. The present study aimed to test the effect of a polyherbal supplement containing ginger and annatto called "ReWin(d)" on the gut microbiota of recreational athletes in a pilot, randomized, triple-blind, placebo-controlled trial. Thirty-four participants who practice physical activity at least three times weekly were randomly allocated to two groups, a ReWin(d) group or a maltodextrin (placebo) group. We evaluated the gut microbiota, the production of short-chain fatty acids, and the serum levels of interleukin-6 and lipopolysaccharide at baseline and after 4 weeks. Results showed that ReWin(d) supplementation slightly increased gut microbiota diversity. Pairwise analysis revealed an increase in the relative abundance of Lachnospira (β -coefficient = 0.013; p = 0.001), Subdoligranulum (β -coefficient = 0.016; p = 0.016), Roseburia (β -coefficient = 0.019; p = 0.001), and Butyricicoccus (β -coefficient = 0.005; p = 0.035) genera in the ReWin(d) group, and a decrease in Lachnoclostridium (β -coefficient = − 0.008; p = 0.009) and the Christensenellaceae R7 group (β -coefficient = − 0.010; p < 0.001). Moreover, the Christensenellaceae R-7 group correlated positively with serum interleukin-6 (ρ = 0.4122; p = 0.032), whereas the Lachnospira genus correlated negatively with interleukin-6 (ρ = − 0.399; p = 0.032). ReWin(d) supplementation had no effect on short-chain fatty acid production or on interleukin-6 or lipopolysaccharide levels. [ABSTRACT FROM AUTHOR]